It can surely have helped. Isolating vibrations can be counted but its very hard so I usually do trial/error. With bad luck you can enhance microphony if you happen to pick the self frequency regarding to weight and isolation material.

Ok, here are the latest findings.
Shaking or taping the box, doesn' t change a thing.
I replaced the choke in one channel with 2X11k resistors in parallel the square wave is perfect.
I am listening what the experts have to say now!
Should I remove the chokes?

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"Without deviations from the norm, progress is not possible" - Frank Zappa